Compact arrays or libraries of surface-bound, double-stranded oligonucleotides are of use in rapid, high-throughput screening of compounds to identify those that bind, or otherwise interact with, short, double-stranded DNA sequence motifs. Of particular interest are proteins, particularly trans-regulatory factors, that control gene transcription. Ideally, such an oligonucleotide array is bound to the surface of a solid support matrix that is of a size that enables laboratory manipulations, e.g. an incubation of a candidate protein with the nucleic acid targets sequences thereon, and that is itself inert to chemical interactions with experimental proteins, buffers and/or other components. In addition, it is desirable that the absolute number of unique target sequences in the array be maximized, since methods of high-throughput screening are used in the attempt to minimize repetition of steps that are labor-intensive or otherwise costly.
A high-density, double-stranded DNA array complexed to a solid matrix is described by Lockhart (U.S. Pat. No.: 5,556,752); however, the DNA molecules therein disclosed are produced as unimolecular products of chemical synthesis. Each member of the array contains regions of self-complementarity separated by a spacer (i.e. a single-strand loop), such that these regions hybridize to each other in order to produce a double-helical region. A difficulty of such a production method arises when the accuracy of chemical synthesis is considered in light to that of that demonstrated by proteinaceous DNA polymerase molecules. It is estimated that enzymatic synthesis of second-strand DNA from a first-strand template operates at 100-fold higher fidelity than do chemical synthetic procedures. Further, it is required that those regions of complementary nucleic acid sequences that must hybridize in order to form the double-helical structure are physically attached to each other by a linker subunit.